Phosphoramidite derivatives, their preparation and the use thereof in the incorporation of reporter groups on synthetic oligonucleotides

ABSTRACT

Phosphoramidite derivatives of formula (V), ##STR1## wherein X is biotin and Y is a protecting group. There may be a linker arm, of variable length, between X and the rest of the molecule. Examples of the protecting group Y include 4,4&#39;-dimethoxytrityl, trifluoroacetyl and fluorenylmethoxycarbonyl (Fmoc). The phosphoramidite derivatives are useful in single or multiple labelling of synthetic oligonucleotides. Process for the preparation of these phosphoramidite derivatives are also disclosed.

This invention relates to certain novel phosphoramidite derivatives,particularly biotinyl and phosphotyrosinyl phosphoramidite derivatives,which are useful in the incorporation of single or multiple reportergroups on synthetic oligonucleotides. Processes for the preparation ofthese phosphoramidite derivatives are also disclosed.

Chemically labelled oligonucleotides are today commonly used ashybridisation probes for the detection of specific gene sequences,including those associated with human genetic diseases. Such probes maybe labelled with biotin and this is highly detectable due to itsaffinity for binding to the proteins avidin and streptavidin. Biotin canthus in some circumstances provide a safer and more convenient form oflabelling than would the use of a radioactive label (such as ³² P). Inaddition to hybridisation probes, biotin-labelled synthetic DNA(particularly 5'-biotinylated oligonucleotides) has found uses inligase-mediated gene detection, direct di-deoxy. sequencing followingthe polymerase chain reaction and the non-radioactive sequencing of DNA.However, the use of such materials has heretofore been restricted by thelack of an efficient and straightforward method for their production.

Numerous methods are known for the attachment of a single biotin moietyor other single reporter groups to the 5'-end of a syntheticoligodeoxyribonucleotide. Most of these involve the use of a linkerphosphoramidite or H-phosphonate as the final coupling step inmachine-aided assembly of the oligonucleotide ¹⁻⁴. After deprotection,an amino, thiol, or other functional group is generated at the 5'-end ofthe oligonucleotide and this group must then be reacted with anactivated biotin derivative in a separate step.

For the attachment of multiple biotins and other labels, the most commonprocedures involve the preparation of a nucleoside derivative speciallyfunctionalised on the heterocyclic base to give a reactive functionalgroup upon deprotection. The functionalised nucleoside is incorporatedeither enzymatically⁵,6 or chemically as a phosphoramiditederivative⁷,8. Once again an extra step is necessary in order to convertthe functional groups into the appropriate polybiotinylated species.More recently, Roget et al⁹ have shown that it is possible to use4-N-(6-N-biotinylaminohexyl)-2^(i) -0-deoxycytidine (or-5-methyl-2'-deoxycytidine) derivatised as a phosphoramidite inmachine-aided assembly of oligonucleotides to generate, upondeprotection, biotinylated nucleotide tails on the 5'-end ofoligonucleotides. A 45-mer oligonucleotide tailed in this way is claimedto be more sensitive in in situ hybridisation using astreptavidin-alkaline phosphatase detection system than the same 45-mertailed at the 3'-end with biotin dUTP by an enzymatic method ¹⁰,although no quantitation was reported.

Cytidine derivatives functionalised on the heterocycle with biotin arenot particularly conveniently prepared in that the 4-thiodeoxynucleosidestarting materials are expensive. Moreover, the use of oligonucleotidetails may limit the stereochemical accessibility of the biotin moietiesor alter the hybridisation properties of the oligonucleotide probe towhich it is attached. Thus the use of a much simpler, non-nucleosidiclinker phosphoramidite reagent capable of allowing the incorporation ofmultiple biotins or other reporter groups would be desirable.

Recently, Nelson et al. ¹¹ have reported that a 3-amino-1,2-propanediolunit can be functionalised to provide a phosphoramidite that can be usedin oligonucleotide assembly. After deprotection, the oligonucleotidecontains a 5'-tail of aliphatic primary amino groups on a repeatingbranched 3-carbon backbone. Whereas five such units can be efficientlyassembled at the 5'-end of an oligonucleotide, only 65% of the aminogroups could be functionalised subsequently with biotin, however. Veryrecently, Haralambidis et al.¹² have reported the incorporation of up to10 biotin residues on the 3'-end of an oligonucleotide by means of acombination of synthetic peptide and oligonucleotide chemistry onsolid-phase. A disadvantage of this approach, however, is that twodifferent machines are required for assembly of thepeptide-oligonucleotide composite. In addition, it is necessary for thebiotin to be conjugated after assembly of the polyamide chain.

In the case of biotin and other chemically stable reporter groups, itwould be advantageous to incorporate the reporter group directly intothe phosphoramidite derivative rather than to have to rely onpost-assembly functionalisation. While there have been two recentlypublished reports of biotinyl linker phosphoramidites having been usedto attach single biotin moieties to the 5'-end of syntheticoligonucleotides¹³,14, to our knowledge no biotinyl linkerphosphoramidite has been described which is capable of allowingincorporation of multiple biotins into a synthetic oligonucleotide.

The object of the present invention is to facilitate the more convenientusage and synthesis of a biotinyl linker phosphoramidite and also alinker phosphoramidite containing the alternative reporter group,phosphotyrosine, which has not hitherto been used in connection withnucleic acid probes.

According to the present invention, there is provided a phosphoramiditederivative of the following formula: ##STR2## wherein X=a reportergroup, and

Y and Z=protecting groups.

The reporter group (X) may comprise any hapten or other detectablemoiety. Examples include: biotin, dinitrophenyl, dansyl andfluoresceinyl. There may be a linker arm, of variable length, betweenthe reporter group and the rest of the molecule. The protecting groups(Y and Z) may comprise, for example, 4,4'-dimethoxytrityl,trifluoroacetyl or fluorenylmethoxycarbonyl (Fmoc).

According to the present invention there is also provided a method forthe production of the above biotinyl phosphoramidite derivative (V) andwhich comprises:

i) Reaction of solketal with acrylonitrile to form the addition product,2-cyanoethyl solketal (I): ##STR3## ii) Reduction of the resultantcompound (I) to form 3-aminopropyl solketal (II): ##STR4## iii) Reactionof the resultant compound (II) with biotin N-hydroxysuccinimide to formN-biotinyl-3-aminopropyl solketal (III): ##STR5## iv) Reaction of theresultant compound (III) with 4,4'-dimethoxytrityl chloride to form1-0-(4,4'-dimethoxytrityl)-3-0-(N-biotinyl-3-aminopropyl) glycerol (IV):##STR6## v) Phosphitylation of the resultant compound (IV) to producethe desired biotinyl phosphoramidite derivative (V): ##STR7## whereinDMTr=4,4'-dimethoxytrityl.

According to the present invention there is also provided a method forthe production of the above phosphotyrosinyl phosphoramidite derivative(XII) and which comprises:

i) Reaction of L-tyrosine benzyl ester with9-fluorenylmethylchloroformate to formN-fluorenylmethoxycarbonyl-L-tyrosine benzyl ester (VI): ##STR8## ii)Phosphitylation of the resultant compound (VI), followed by oxidation toform N-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl)phosphate]-L-tyrosine benzyl ester (VII): ##STR9## iii) Debenzylation ofthe resultant compound (VII) to form N-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl)phosphate]-L-tyrosine (VIII): ##STR10## iv) Reaction of theresultant compound (VIII) with pentafluorophenyl to form thecorresponding pentafluorophenyl derivative (IX): ##STR11## v) Couplingthe resultant compound (IX) to 3-aminopropyl solketal (II), removing theisopropylidene group from the resultant solketal derivative, followed byreaction of the product with 4,4'-dimethoxytrityl chloride and thenphosphitylation of the product thereof to produce the desiredphosphotyrosinyl phosphoramidite derivative (XII): ##STR12## whereinDMTr=4,4'-dimethoxytrityl and ##STR13##

According to a still further embodiment the present invention provides amethod for the single or multiple labelling of syntheticoligonucleotides and which comprises the use of the aforementionedbiotinyl phosphoramidite derivative (V) or phosphotyrosinylphosphoramidite derivative (XII). It is to be understood that theincorporation of the single or multiple label may occur at either the 5'end or the 3' end of the oligonuleotide or at any point along the chain.

A variety of uses are envisaged for the phosphoramidite derivatives.These include use for preparing oligonucleotides which may be used ashybridisation probes; for the capture of nucleic acids onto solidsupport matrices resulting from solid phase or solution phasehybridisation reactions; as primers in the polymerase chain reaction(PCR); as primers in nucleic acid sequencing reactions; in theproduction of affinity matrices for the purification of DNA bindingproteins and other biomolecules; in the production of affinity matricesfor the detection of nucleic acid sequences; as a means of monitoringincorporation reactions; in producing a random selection of labelledprobes for the detection of the total nucleic acid content of samples byhybridisation; in a sandwich hybridisation system where one labelledprobe acts as a capture and a probe with an alternative label acts as areporter; for providing a biotinylated or haptenylated oligonucleotidefor use in any DNA manipulation protocol; in cloning recombinant DNA andin invitro mutagenesis.

The phosphoramidite derivatives of this invention contain a repeatinglinker unit and, in both cases, this comprises a simple 3-carbonglyceryl backbone which gives maximum flexibility as well as goodaqueous solubility properties. The preparation of the compounds will nowbe described in greater detail and with reference to Reaction Scheme 1(biotinyl phosphoramidite) and Reaction Scheme 2 (phosphotyrosinylphosphoramidite) respectively.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1 to 7 show results for isolation of oligonucleotides as describedin Scheme 2, by reverse phase liquid chromatography or preparativepolyacrylamide gel electrophoresis.

FIG. 8 shows the effect of biotin tail length on efficiency of DNAcapture--Experiment 1.

FIG. 9 shows the effect of biotin tail length on efficiency of DNAcapture--Experiment 2.

FIG. 10 shows signal strength for ECL detection of 5 ng of M13 DNA foreach of five biotinylated probes.

A=1 biotin

B=2 biotins

C=4 biotins

D=8 biotins

E=4 biotins spaced with 3 thymidines

F=Probe labelled directly with horseradish peroxidase.

FIG. 11 shows signal strength for ECL detection of 10 ng of M13 DNA foreach of five phosphotyrosinylated probes.

A=1 phosphotyrosine

B=2 phosphotyrosines

C=4 phosphotyrosines

D=8 phosphotyrosines

E=4 phosphotyrosines spaced with 3 thymidines.

SCHEME 1

Reaction of readily available solketal with acrylonitrile in thepresence of sodium hydride in tetrahydrofuran afforded the additionproduct, 2-cyanoethyl solketal (I), in 79% yield. Reduction of nitrile(I) required carefully controlled conditions since it was found that theuse of strong reductants (such as lithium aluminium hydride) causepreferential elimination. Best results were found using sodiumborohydride in the presence of cobalt (II) chloride in methanolicsolution ¹⁵ to afford 3-aminopropyl solketal which was purified bydistillation in 43% yield. Reaction of amine (II) with biotinN-hydroxysuccinimide in DMF solution gave N-biotinyl-3-aminopropylsolketal (III) in 89% yield.

Biotin derivative (III) was treated with a mixture of 1M hydrochloricacid and tetrahydrofuran (1:1) to remove the isopropylidine group and,without isolation, the product was reacted with 4,4'-dimethoxytritylchloride in anhydrous pyridine to give1-0-(4,4'-dimethoxytrityl)-3-0-(N-biotinyl-3-aminopropyl)glycerol (IV)which was purified by silica column chromatography in 63% yield.Phosphitylation of compound (IV) was carried out using an equimolarproportion of 2-cyanoethyl N,N-diisopropylaminochlorophosphite¹⁶ intetrahydrofuran in the presence of N,N-diisopropylethylamine. Underthese conditions, the predominant product was the desired singlyphosphitylated product,1-0-(4,4'-dimethoxytrityl)-3-0-(N-biotinyl-3-aminopropyl)glyceryl2-0-(N,N-diisopropylamino)phosphite (V), which was readily separated bysilica column chromatography in 58% yield. ³¹ p nmr of compound V showedjust four peaks of approximately equal intensity corresponding to thefour possible diastereomers. Analytical reversed-phase HPLC showed morethan 90% of the UV absorption in two closely eluting peaks eachpresumably corresponding to a pair of diastereomers.

Starting compound IV was also recovered as a later eluting fraction fromthe silica column in 32% yield. A small amount of doubly phosphitylatedproduct was observed in the crude reaction product, the formation ofwhich was considerably exacerbated by the use of excess phosphitylatingagent. ³¹ p nmr evidence suggested that this contaminant contained onephosphite moiety attached to the biotin ring at N-3, which is in linewith the findings of Alves et al¹³.

SCHEME 2

To prepare a suitable phosphoramidite derivative containing tyrosinephosphate, it was necessary to consider the question of protection ofthe phosphate group of tyrosine. By analogy with nucleoside phosphatederivatives, it was thought that bis(2-cyanoethyl) protection shouldafford sufficient stability under acidic conditions yet should beremovable with aqueous ammonia under conditions needed to remove baseprotecting groups. For N-protection, the fluorenylmethoxycarbonyl groupwas chosen¹⁹.

Reaction of L-tyrosine benzyl ester with 9-fluorenylmethyl-chloroformatein pyridine at 0° C. afforded after crystallisation an 84% yield ofN-fluorenylmethoxycarbonyl-L-tyrosine benzyl ester (VI). Phosphitylationof compound VI with bis(2-cyanoethyl)-N,N-diisopropylaminophosphine inacetonitrile in the presence of tetrazole followed by oxidation with3-chloroperbenzoic acid gave an 86% yield of crystallineN-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl) phosphate]-L-tyrosinebenzyl ester (VII). Debenzylation of compound VII was accomplished withhydrogen (Pd/C). Concomitant loss of the fluorenylmethoxycarbonyl groupwas minimised by use of ethyl acetate as a co-solvent with ethanol.Small amounts of liberated dibenzofulvene were removed by diethyl etherextraction and the desiredN-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl) phosphate]-L-tyrosine(VIII) was purified by extraction from acidic solution into ethylacetate and isolated in 65% yield.

The tyrosine phosphate derivative VIII when treated with a mixture of0.1M hydrochloric acid and tetrahydrofuran (1:1) at room temperature for3 hours gave less than 5% loss of the phosphate group. Treatment ofcompound VIII with concentrated ammonia in a sealed tube for 5 hours at60° C. gave rise to complete removal of both 2-cyanoethyl groups withonly a trace of loss of phosphate.

Reaction of compound VIII with pentafluorophenol in the presence ofdicyclohexylcarbodiimide in dioxane solution gave the correspondingpentafluorophenyl derivative (IX) in 82% yield. IX was coupled to3-aminopropyl solketal (II) in DMF solution to give after silica columnchromatography an 86% yield ofN-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl)phosphate]-L-tyrosinyl-3-aminopropyl solketal (X). The isopropylidenegroup of the solketal derivative X was removed using 1M hydrochloricacid/tetrahydrofuran and without isolation the product was reacted inpyridine solution with 4,4'-dimethoxytrityl chloride to give aftersilica column chromatography1-0-(4,4'-dimethoxytrityl)-3-0-(N-[N-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl)phosphate]-L-tyrosinyl]-3-aminopropyl)glycerol(XI) in 70% yield. Phosphitylation of compound XI by 2-cyanoethylN,N-diisopropylaminochlorophosphite in the presence ofN,N-diisopropylethylamine gave after silica column chromatography thecorresponding 2-0-(N,N-diisopropylamino)(2-cyanoethyl)phosphitederivative (XII) as a solid foam in 44% yield. The ³¹ p nmr spectrum ofcompound XII showed a doublet at δ-148.65 and 148.64 corresponding tothe tyrosyl phosphate and three peaks at δ7.41, 7.68 and 7.96 in theratio of 1:1:2. These latter 3 signals are presumably accounted for byonly partial resolution of the expected 4 diasteromers due to chiralityat the C-2 of the glyceryl moiety and the P of the phosphite group.##STR14##

The phosphoramidite (V) was used in the final coupling steps inoligonucleotide assembly by the phosphoramidite procedure¹⁷ using anApplied Biosystems 380B 3-column DNA synthesiser. Three parallelassemblies were carried out of the 17-mer d(GTAAAACGACGGCCAGT)(corresponding to the sequence of the universal M13 sequencing primer¹⁸with respectively one, two and four extra cycles of coupling withphosphoramidite (V) after the assemblies of the core oligonucleotide17-mers. The efficiency of addition of phosphoramidite (V) averaged 99%as judged by release of dimethoxytrityl cation before subsequentcoupling steps. The final terminal dimethoxytrityl group in assembly wasnot removed. This was to maintain the terminal primary hydroxyl group ina masked configuration in order to prevent, during subsequent ammoniatreatment, attack of the terminal hydroxyl group of the glyceryl moietyon the nearest phosphate linkage giving rise to elimination of theterminal glyceryl unit.

After complete deprotection, the three 17-mers were purified by reversedphase chromatography and in each case a major component corresponding tothe desired product was seen (FIGS. 1, 2 and 3). It can be seen that thesingly biotinylated 17-mer (bio)₁ -17 was retarded in mobility comparedto an unbiotinylated control. The doubly biotinylated 17-mer (bio)₂ -17was further retarded and the quadruply biotinylated 17-mer (bio)₄ -17was still further retarded. Thus, reversed phase chromatography is aconvenient system for both purification and for assessment of thehomogeneity of biotinylated oligonucleotides. Overall isolated yieldsafter assembly and purification were 26, 25 and 19% respectively for(bio)₁ -17, (bio)₂ -17 and (bio)₄ -17 respectively based on the amountof first nucleoside attached to the support.

A 5'-tail of eight biotins was also prepared by assembly of the same17-mer followed by 8 sequential additions of the biotinyl linker (V)which afforded after deprotection a 19% overall isolated yield of the(bio)₈ -17 after reversed-phase chromatography. In order to determinethe effect of further spacing of biotin residues, another assembly ofthe 17-mer was carried out followed by four additions of biotin linkerinterspersed with three thymidyl residues. The isolated yield of(bio-dT)3-bio-17) was 19% after reversed-phase purification.

The phosphotyrosyl linker XII was used in oligonucleotide assembly ofthe following derivatives of the 17-long M13 primer: (PTyr)₁ -17,(PTyr)₂ -17, (PTyr)₄ -17, the thymidyl spaced derivative(PTyr-dT)3-PTyr-17, and (PTyr)₈ -17. Average coupling yields for thephosphotyrosyl linker as judged by analysis of liberated dimethoxytritylgroups were 96%. In the cases of the first four oligonucleotides,isolation was by ion exchange HPLC (FIGS. 4, 5, 6 and 7) making use ofthe extraformal negative charges on the phosphotyrosine moieties to aidseparation (isolated yields of 16, 8, 13 and 14% respectively), whereasfor the (PTyr)₈ -17 preparative polyacrylamide gel electrophoresis wasused (isolated yield 14%).

The present invention is further illustrated by the following Examples.

EXAMPLE 1

Pyridine, acetonitrile and N,N-diisopropylethylamine were dried bydistillation from calcium hydride. Tetrahydrofuran and dioxane weredried by distillation from sodium/benzophenone. N,N-dimethylformamide(DMF) was dried by distillation under reduced pressure (18 mm Hg).Biotin N-hydroxysuccinimide was prepared from biotin by the method ofBecker et al (20). L-Tyrosine benzyl ester p-toluenesulphonate salt wasobtained from Sigma and 9-fluorenylmethyl-chloroformate from Fluka.Bis(2-cyanoethyl)-N,N-diisopropylaminophosphine was obtained fromdichloro-N,N-diisopropylaminophosphine (Aldrich) by the method ofUhlmann and Engels (21). Organic solutions were dried over anhydroussodium sulphate. Column chromatography was carried out by the shortcolumn method using Kieselgel 60H (Merck).

Melting points were measured on a Koefler hot stage apparatus and areuncorrected. Thin layer chromatography (t.l.c.) was carried out usingKieselgel 60 F254 plates (Merck) with aluminium backing and devolpmentwith the following solvents: A, chloroform/absolute ethanol (19:1); B,chlorofom/ethanol (9:1); C, chloroform/ethanol (4:1); D,acetonitrile/methanol (4:1); E, methylene chloride/methanol (9:1)containing 1% pyridine; F, chloroform/ethanol (39:1); G,chloroform/ethanol (9:1) containing 2% acetic acid; H, methylenechloride/methanol (19:1); I, methylene chloride/ethyl acetate (1:1)containing 1% 2,6-lutidine. Plates were visualised under shortwaveultraviolet light, with iodine vapour, or by spraying with 2% ethanolicmolybdophosphoric acid. Dimethoxytrityl-containing compounds werevisualised by exposing the t.l.c. plate to vapour of concentratedhydrochloric acid. Biotin-containing derivatives were visualised byspraying with a reagent containing p-dimethylaminocinnamaldehyde (22).

Proton nuclear magnetic resonance (nmr) spectra were recorded on aBruker WM-250 spectrometer (250 MHz) with chemical shifts given relativeto tetramethylsilane and ³¹ P-nmr were recorded on a Bruker AM-400spectrometer (162 MHz) with chemical shifts given relative to trimethylphosphite. All spectra were taken with compounds as deuterochloroformsolutions unless otherwise stated. Mass spectra were recorded on aKratos model MS 890 spectrometer for fast atom bombardment (FAB)ionisation using 3-nitrobenzylalcohol as matrix and on a Kratos MS 902spectrometer for electron impact (EI) ionisation.

Reversed-phase h.p.l.c. was carried out on an analytical or asemipreparative μ Bondapak C18 reversed phase column (Waters) usinggradients of buffer A (0.1M ammonium acetate solution) and buffer B (20%buffer A/80% acetonitrile) at flow rates of 1.5 ml/min (analytical runs)or 3 ml/min (purification runs). Ion exchange h.p.l.c. was carried outon an analytical Partisphere 5-SAX cartridge (Whatman) using gradientsof potassium phosphate buffer (pH 6.3) containing 60% formamide.

2-Cyanoethyl solketal (I)

Solketal (2,2-dimethyl-1,3-dioxolane-4-methanol) (26.4 g, 200 mmole) andacrylonitrile (26.4 ml, 400 mmole) were dissolved in dry tetrahydrofuran(500 ml). To the stirred and cooled (waterbath) solution, sodium hydride(0.96 g, 40 mmole) was added in two portions and stirring was continuedfor 1 hour. Then water (100 ml) was added dropwise and the resultantsuspension was concentrated to remove tetrahydrofuran. Water (200 ml)was again added and the mixture was extracted with methylene chloride(2×300 ml). The extracts were dried and concentrated to give an oil(44.06 g) which was distilled under reduced pressure to give the titlecompound (23.42 g, 79% yield) as an oil (bp. 96°-97° C. at 0.5 mmHg.).T.l.c. in Solvent A, R_(f) 0.76. ¹ H nmr, δ:1.35(s, 3H), 1.41(s,3H), 2.61(t, J=6.3 Hz, 2H), 3.51-3.58 (m, 2H), 3.69-3.76 (m, 3H), 4.05(dd, J=8.2 Hz, J=6.4 Hz, 1H), 4.23 (quintet, J=5.5 Hz, 1H). MassSpectrum (EI), m/z 186 (M⁺. +1).

3-Aminopropyl solketal (II)

2-Cyanoethyl solketal (I)(27.75 g, 150 mmole) was dissolved in methanol(900ml) and cobalt(II) chloride.6H₂ O (71.37 g, 0.3 mole) was added. Tothis stirred and cooled (waterbath) solution was added sodiumborohydride (56.76 g, 1.5 mole) in two portions (caution, foaming).Stirring was continued for 1 hour and then concentrated ammonia solution(300 ml) was added. The resultant suspension was filtered andconcentrated to remove methanol. The mixture was extracted withchloroform (2×300 ml) and the extracts dried and evaporated to give anoil (20.82 g) which was distilled under reduced pressure to yield thetitle compound (12.12 g, 43% yield) as an oil (bp. 78°-9° C. at 0.5 mmHg). T.l.c. in Solvent B, R_(f) 0.10. ¹ H-nmr, δ: 1.34 (s, 5H), 1.40 (s,3H), 1.70 (quintet, J=6.5 Hz, 2H), 2.77 (t, J=6.8 Hz, 2H), 3.38-3.57 (m,4H), 3.70 (dd, J=8.2 Hz, J=6.3 Hz, 1H), 4.03 (dd, J=8.2 Hz, J=6.3 Hz,1H), 4.24 (quintet, J=5.8 Hz, 1H). Mass Spectrum (EI), m/z 190 (M⁺. +1).

N-Biotinyl-3-aminopropyl solketal (III)

Biotin N-hydroxysuccinimide ester (3.41 g, 10 mmole) was dissolved inhot dry DMF (40 ml). After cooling, a solution of 3-aminopropyl solketal(II) (2.27 g, 12 mmole) in dry DMF (20 ml) was added dropwise withstirring. The solution was left for 1 hour and then concentrated. Theresidue was dissolved in chloroform (100 ml) and washed with saturatedsodium bicarbonate solution (50 ml). The aqueous layer was washed withchloroform (50 ml) and the chloroform extracts were combined, dried andconcentrated. The resultant solid was washed with pentane (40 ml),filtered off and dried to give the title compound (3.71 g, 89% yield) ascrystals (mp. 126°-7° C.). T.l.c. in Solvent C, R_(f) 0.38. ¹ H-nmr, δ:1.35 (s, 3H), 1.42 (s, 3H), 1.42 (quintet, J=7.2 Hz, 2H), 1.61-1.82 (m,6H), 2.19 (t, J=7.5 Hz, 2H), 2.81 (d, J=12.8 Hz, 1H), 2.90 (dd, J=12.8Hz, J=4.8 Hz, 1H), 3.10-3.16 (m, 1H), 3.31-3.36 (m, 2H), 3.48 (d, J=5.2Hz, 2H), 3.57 (t, J=5.4 Hz, 2H), 3.71 (dd, J=8.2 Hz, J=6.2 Hz, 1H), 4.05(dd, J=8.1 Hz, J=6.4 Hz, 1H), 4.25-4.33 (m, 2H), 4.48-4.53 (m, 1H), 5.46(br. s, 1H), 6.28 (br.s, 1H), 6.53 (br. s, 1H). Mass spectrum (+FAB),m/z 416.3 (M⁺. +1).

1-O-(4,4'-dimethoxytrityl)-3-O-(N-Biotinyl-3-aminopropyl) glycerol (IV)

N-biotinyl-3-aminopropyl solketal (III) (2.50 g, 6 mmole) was disolvedin a mixture of tetrahydrofuran (12 ml) and 1M hydrochloric acid (12ml). The solution was left for 0.5 h and then absolute ethanol (12 ml)was added. The solution was concentrated, the residue was dissolved inabsolute ethanol (12 ml) and concentrated again. The resultant productwas dried by co-evaporation with pyridine (2×12 ml) to give an oil (2.46g) which was redissolved in dry pyridine (24 ml) and4,4'-dimethoxytrityl chloride (2.03 g, 6 mmole) added in a two portionswith stirring. Stirring was continued for 15 min and the resultantsolution was left for 1 hour. Absolute ethanol (12 ml) was added and thesolution was concentrated. The residue was dissolved in chloroform (60ml and washed with saturated sodium bicarbonate solution (30 ml). Theaqueous layer was washed with chloroform (30 ml) and the chloroformextracts were combined, dried and evaporated to an oil (5.28 g). Theproduct was chromatographed on a silica column (120 g) eluting withacetonitrile/methanol (9:1) and then acetronitrile/methanol (4:1).Fractions containing a single component were collected and evaporated todryness to yield the title compound (2.55 g, 63% yield) as a foam.T.l.c. in Solvent D, R_(f) 0.39. ¹ H-nmr, δ: 1.36-1.42 (m, 2H),1.61-1.73 (m, 6H), 2.12-2.20 (m, 2H), 2.62 (d, J=12.8 Hz), 2.79-2.86 (m,1H), 3.03-3.21 (m, 3H), 3.28-3.34 (m, 2H), 3.46-3.58 (m, 4H), 3.77 (s,6H), 3.93-3.96 (m, 1H), 4.15-4.24 (m, 1H), 4.35-4.41 (m, 1H), 5.43 (br.s, 1H), 5.43 (br. s, 1H), 6.61 (br. s, 1H), 6.78 (br. s, 1H), 6.78-6.82(m, 4H), 7.18-7.43 (m, 9H). Mass Spectrum (+FAB), m/z 678.4 (M⁺. +1).

1-O-(4,4'dimethoxytrityl)-3-O-(N-biotinyl-3-aminopropyl)glyceryl2-O-(N,N-diisopropylamino)cyanoethyl phosphite (V).

1-O-(4,4'-dimethoxytrityl)-3-O-(N-biotinyl-3-aminopropyl)glycerol (IV)(1.36 g, 2 mmole) was dissolved in dry tetrahydrofuran (4 ml) andN,N-diisopropylethylamine (0.52 ml, 3 mmole) was added. Then a solutionof 2-cyanoethyl N,N-diisopropylaminochlorophosphite (0.47 g, 2 mmole) indry tetrahydrofuran (1 ml) was added dropwise with stirring. Thereaction mixture was left for 1 h, filtered, and the filtrate wasdiluted with ethyl acetate (100 ml). The resultant solution was washedwith 0.5M phosphate buffer pH 7.0 (2×20 ml), dried and concentrated. Theresidue (1.92 g) was chromatographed on a silica column (60g) elutingwith methylene chloride/methanol (39:1) and then methylenechloride/methanol (19:1) both containing 1% triethylamine. Two fractionswere collected. The faster eluting product was evaporated to gave a foam(1.10 g) which was dissolved in toluene (10 ml) and precipitated intopentane (200 ml). The precipitate was washed with pentane (200 ml),collected by centrifugation, and dried. The title compound (1.02 g, 58%yield) was obtained as a fine powder. T.l.c. in Solvent E, R_(f) 0.33. ¹H-nmr, δ: 1.01-1.18 (m, 12H), 1.39 (quintet, J=7.2 Hz, 2H), 1.62-1.70(m, 6H), 2.07-2.14 (m, 2H), 2.45 (t, J=6.5H2, 1H), 2.63 (t, J=6.5 Hz,1H), 2.65 (d, J=13.0 Hz, 1H), 2.87 (dd, J=12.8 Hz, J=4.8 Hz, 1H),3.07-3.34 (m, 5H), 3.47-3.75 (m, 8H), 3.77 (s, 3H), 3.88 (s, 3H),4.07-4.13 (m, 1H), 4.24-4.29 (m, 1H), 4.43-4.48 (m, 1H), 5.04 (br.s,1H), 5.74 (br.s, 1H), 6.22 (br.d, J=18.4 Hz, 1H), 6.78-6.83 (m, 4H),7.18-7.45 (m, 9H). ³¹ P-nmr, δ: 6.09, 6.12, 7.61, 7.63. Mass Spectrum(+FAB) 876.4 (M⁺. -1). Elemental analysis, found: C, 63.10; H, 7.62; N,7.84; calculated for C₄₆ H₆₄ N₅ O₈ P: C, 62.92; H, 7.35; N, 7.98. Hplcusing isocratic elution at 90% buffer B showed two closely eluting peakscorresponding two two pairs of diastereoisomers (R_(t) 4.82 and 5.16min).

Fractions containing the slower eluting product were evaporated todryness to give unreacted starting compound IV (0.44 g, 32% recovery).

N-Fluorenylmethoxycarbonyl-L-tyrosine benzyl ester (VI)

L-Tyrosine benzyl ester p-toluenesulphonate salt (11.09 g, 25 mmole) wasdissolved in dry pyridine (125 ml). The solution was cooled in anice/water bath and then 9-fluorenylmethyl-chloroformate (6.47 g; 25mmole) was added with stirring. Stirring was continued for 1 hour at 0°C. and for 1 hour at room temperature. The reaction mixture wasconcentrated, dissolved in toluene (50 ml) and concentrated once more togive an oil (24.0 g). Crystallization from acetonitrile (50 ml) gave aninitial crop of 6.85 g. The filtrate was concentrated and the resultantoil was dissolved in chloroform (200 ml) and washed with 0.5Mhydrochloric acid (50 ml). The aqueous layer was extracted withchloroform (2×50 ml) and the chloroform extracts were combined, driedand evaporated to dryness. The resultant crystalline solid (6.77 g) wascombined with the first crop and recrystallized from acetonitrile (60ml) to yield the title compound (10.38 g, 84% yield): mp. 150°-1° C.T.l.c. in Solvent F, R_(f) 0.48. ¹ H nmr (d₆ DMSO), δ: 2.85-2.93 (m,2H), 3.32 (d, J=12.2 Hz, 1H), 4.18-4.25 (m, 4H), 5.09 (s, 2H), 6.25 (d,J=8.4 Hz, 2H), 7.03 (d, J=8.4 Hz, 2H), 7.26-7.44 (m, 8H), 7.63-7.67 (m,2H), 7.87-7.93 (m, 3H), 9.25 (m, 1H). Mass spectrum (+FAB), m/z 494.2(M⁺. +1).

N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)-phosphate]-L-tyrosinebenzyl ester (VII)

N-Fluorenylmethoxycarbonyl-L-tyrosine benzyl ester (VI) (7.41 g, 15mmole) and 1H-tetrazole (1.58 g, 22.5 mmole) were dissolved in dryacetonitrile (225 ml) and then a solution ofbis(2-cyanoethyl)-N,N-(diisopropylamino)phosphine (6.10 g, 22.5 mmole)in dry acetonitrile (22.5 ml) was added dropwise with stirring. Thereaction mixture was left for 1 hour and then 50% 3-chloroperbenzoicacid (5.16 g, 15 mmole) was added with stirring and cooling by use of awater bath. Stirring was continued at room temperature for 0.5 hour andthe solution was concentrated to an oil (13.50 g). the oil was dissolvedin chloroform (450 ml) and washed with saturated sodium bicarbonatesolution (225 ml). The chloroform solution was dried, evaporated todryness to give an oil (14.80 g). Crystallization from a mixture ofmethylene chloride (60 ml) and diethyl ether (120 ml) gave the titlecompound (8.80 g, 86% yield): mp. 103°-4° C. T.l.c. in Solvent A, R_(f)0.44. ¹ H nmr, δ: 2.65-2.73 (m, 2H), 4.19 (t, J=6.8 Hz, 1H), 4.2 8-4.47(m, 6H), 4.68 (dt, J=12.1 Hz and J=5.7 Hz, 1H), 5.12 (d, J=12.1 Hz, 1H),5.19 (d, J=12.1 Hz, 1H), 5.36 (d, J=12.1 Hz, 1H), 6.97 (d, J=8.3 Hz,2H), 7.07 (d, J=8.3 Hz, 2H), 7.27-7.43 (m, 9H), 7.57 (d, J=7.0 Hz, 2H),7.76 (d, J=7.4 Hz, 2H). ³¹ P nmr, δ: -148.60. Mass spectrum (+FAB), m/z680.3 (M⁺. +1).

N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)-phosphate]-L-tyrosine(VIII)

N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)phosphate]-L-tyrosinebenzyl ester (VIII) (6.80 g, 10 mmole) was dissolved in a mixture of 95%ethanol (200 ml) and ethyl acetate (200 ml) and 10% palladium oncharcoal (1.0 g) was added. The suspension was stirred under hydrogenuntil nearly all the substrate was gone (T.l.c. assay). The reactionmixture was filtered and the filtrate was concentrated. The resultantoil (6.20 g) was dissolved in a 1% solution of sodium carbonate (200 ml)and the solution was shaken with diethyl ether (100 ml). The aqueoussolution was acidified with citric acid to pH4 and the resultantsuspension was extracted with ethyl acetate (200 ml). The organic phasewas dried and evaporated to give the title compound (3.83 g, 65% yield)as a solid foam. T.l.c. in Solvent G, R_(f) 0.38. ¹ H nmr, δ: 2.71 (t,J=6.0 Hz, 4H), 3.13 (d, J=5.3 Hz, 2H), 4.20 (t, J=6.7 Hz, 1H), 4.30-4.51(m, 6H), 4.65 (dt, J=12.0 Hz and J=5.4 Hz, 1H), 5.48 (d, J=12.1 Hz, 1H),7.13, (s, 4H), 7.28-7.43 (m, 4H), 7.58 (d, J=7.2 Hz, 2H), 7.77 (d, J=7.4Hz, 2H). ³¹ P nmr, δ: -148.85. Mass spectrum (+FAB), m/z 590.2 (M⁺. +1).

N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)-phosphate]-L-tyrosinepentafluorophenyl ester (IX)

N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)-phosphate]-L-tyrosine(VIII) (2.95 g, 5 mmole) was dissolved in dry dioxane (20 ml) and asolution of pentafluorophenol (1.02 g, 5.5 mmole) in dry dioxane (5 ml)was added. Then dicyclohexylcarbodiimide (1.13 g, 5.5 mmole) was addedwith stirring. Stirring was continued for 1 hour and the resultantsuspension was filtered. The filtrate was concentrated to an oil (4.18g) which was dissolved in chloroform (100 ml) and washed with saturatedsodium bicarborate solution (50 ml). The organic phase was dried andconcentrated to an oil (3.52 g). The product was chromatographed on asilica column (60 g) eluting with chloroform/ethanol (39:1) and thenchloroform/ethanol (19:1). Fractions containing a single component werecollected and evaporated to dryness to yield the title compound (3.10g,82% yield) as a solid foam. T.l.c. in Solvent A, R_(f) 0.33. ¹ H nmr,δ: 2.74 (t, J=6.0 Hz, 4H), 3.27 (d, J=5.8 Hz, 2H), 4.21 (t, J=6.6 Hz,1H), 4.32-4.48 (m, 6H), 4.97-5.02 (m, 1H), 5.45 (d, J=8.5 Hz, 1H), 7.20(s, 4H), 7.28-7.43 (m, 4H), 7.56-7.59 (m, 2H), 7.77 (d, J=7.4 Hz, 2H).³¹ P nmr, δ: -148.67. Mass spectrum (+FAB), m/z 756.1 (M⁺. +1).

N-{N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)-phosphate]-L-tyrosinyl}-3-aminopropylsolketal (X)

N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)-phosphate]-L-tyrosinepentafluorophenyl ester (LX) (3.02 g, 4 mmole) was dissolved in dry DMF(20 ml). Then a solution of 3-aminopropyl solketal (II) (0.91 g, 4.8mmole) in dry DMF (8 ml) was added dropwise with stirring. The reactionmixture was left for 0.5 hours and then concentrated to an oil (5.61 g)which was dissolved in chloroform (80 ml) and washed with saturatedsodium bicarbonate solution (40 ml). The organic phase was dried andconcentrated to an oil (4.10 g). The product was chromatographed on asilica column (100 g) eluting with chloroform/ethanol (39:1) and thenchloroform/ethanol (19:1). Fractions containing a single component wereevaporated to dryness to give the title compound (2.60 g, 86% yield) asa thick oil. T.l.c. in Solvent A, R_(f) 0.26. ¹ H nmr, δ: 1.40 (s, 3H),1.65 (s, 3H), 1.87-1.90 (m, 2H), 2.76 (t, J=6.1 Hz, 4H), 2.95-3.11 (m,2H), 3.32-3.56 (m, 9H), 4.16-4.20 (m, 1H), 4.32-4.40 (m, 7H), 5.63-5.82(m, 1H), 6.56-6.81 (m, 1H), 7.11-7.16 (m, 4H), 7.28-7.43 (m, 4H), 7.56(d, J=7.4 Hz, 2H), 7.76 (d, J=7.4 Hz, 2H). ³¹ P nmr, δ: -148.65,-148.49.

1-O-(4,4'-dimethoxytrityl)-3-O-(N-{N-fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)phosphate]-L-tyrosinyl}-3-aminopropyl)glycerol (XI)

N-{N-Fluorenylmethoxycarbonyl-O-[bis(2-cyanoethyl)phosphate]-L-tyrosinyl}-3-aminopropylsolketal (X) (2.28 g, 3 mmole) was dissolved in a mixture oftetrahydrofuran (12 ml) and 1M hydrochloric acid (6 ml). The solutionwas left for 1 hour and then absolute ethanol (12 ml) was added. Thesolution was concentrated, the residue was dissolved in absolute ethanol(12 ml) and concentrated again. The resultant product was dried byco-evaporation with pyridine (2×6 ml) to give an oil (2.20 g) which wasredissolved in dry pyridine (12 ml) and 4,4'-dimethoxytritylchloride(1.02 g, 3 mmole) was added with stirring. Stirring was continued for 15mins and the resultant solution was left for 1 hour. Absolute ethanol (6ml) was added and the solution was concentrated. The residue wasdissolved in chloroform (60 ml) and washed with saturated sodiumbicarbonate solution (30 ml). The organic phase was dried and evaporatedto an oil (4.32 g). The product was chromatographed on a silica column(90 g) eluting with methylene chloride/methanol (39:1) and thenmethylene chloride/methanol (19:1). Fractions containing a singlecomponent were collected and evaporated to dryness to yield the titlecompound (2.15 g, 70% yield) as a solid foam. T.l.c. in Solvent H, R_(f)0.28. ¹ H nmr, δ: 1.61-1.67 (m, 2H), 2.66 (q,J=5.7 Hz, 2H), 2.76 (t,J=6.0 Hz, 2H), 3.03-3.14 (m, 4H), 3.29-3.52 (m, 7H), 3.74 (s, 3H), 3.79(s, 3H), 3.88 (br s, 1H), 4.23-4.40 (m, 8H), 5.56-5.82 (m, 1H),6.56-6.68 (m, 1H), 6.78 (d, J=8.9 Hz, 2H), 6.82 (d, J=9.0 Hz, 2H),7.13-7.54 (m, 19H), 7.72-7.78 (m, 2H). ³¹ P nmr, δ: -148.59, -148.57.Mass spectrum (+FAB), m/z 1022.6 (M⁺.).

1-0-(4,4'-dimethoxytrityl)-3-0-(N-{N-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl)phosphate]-L-tyrosinyl}-3-aminopropyl)glyceryl2-0-(N,N-diisopropylamino)(2-cyanoethyl)phosphite (XII).

1-O-(4,4'-dimethoxytrityl)-3-O-(N-{N-fluorenylmethoxycarbonyl-0-[bis(2-cyanoethyl)phosphate]-L-tyrosinyl}-3-aminopropyl)-glycerol(XI) (2.04 g, 2 mmole) was dissolved in dry tetrahydrofuran (4 ml) andN,N-diisopropylethylamine (0.70 ml, 4 mmole) was added. Than a solutionof 2-cyanoethyl N,N-diisopropylamino-chlorophosphite (0.71 g, 3 mmole)in dry tetrahydrofuran (2 ml) was added dropwise with stirring. Thereaction mixture was left for 1 hour, filtered and the filtrate wasdiluted with ethyl acetate (100 ml). The resultant solution was washedwith 0.5M phosphate buffer pH 7.0 (2×20 ml), dried and concentrated. Theresidue (2.52 g) was chromatographed on a silica column (80 g) elutingwith methylene chloride/ethyl acetate (3:1) and then methylenechloride/ethyl acetate (1:1), both containing 1% of 2,6-lutidine.Fractions containing a single component were collected and evaporated todryness. The resultant oil (1.62 g) was dissolved in toluene (16 ml) andproduct precipitated with pentane (320 ml). The precipitate was washedwith pentane (2×320 ml), collected by centrifugation, and dried. Thetitle compound (1.08 g, 44% yield) was obtained as a fine powder. T.l.c.in Solvent I, R_(f) 0.26. 1H nmr, δ: 1.14-1.33 (m, 12H), 1.56-1.75 (m,2H), 2.54-2.79 (m, 6H), 2.93-3.26 (m, 6H), 3.38-3.61 (m, 7H), 3.76 (s,6H), 4.05-4.42 (m, 10H), 5.44-5.60 (m, 1H), 6.21-6.33 (m, 1H), 6.79-6.83(m, 4H), 7.27-7.57 (m, 19H), 7.76 (d, J=7.6 H_(z), 2H). 31P nmr, δ:-148.65, -148.64, 7.41, 7.68, 7.96. Mass spectrum (+FAB), m/z 1223.9 (M⁺+1). Elemental analysis, found: C, 64.70,H, 6.34, N, 6.92; calculatedfor C₆₆ H₇₆ N₆ O₁₃ P₂ : C, 64.81,H, 6.26, N, 6.87. Reversed-phase HPLCusing isocratic elution at 90% Buffer B showed two closely eluting peakscorresponding to two pairs of diastereomers (R_(t) 6.14 and 6.86 min).

Oligonucleotide Assembly

Oligonucleotides were assembled using an Applied Biosystems 380B3-column DNA Synthesiser following manufactures recommendations with thecyanoethyl phosphoramidite procedure. 0.2 μmole scale columns were usedthroughout. For couplings with biotinyl phosphoramidite V orphosphotyrosinyl phosphoramidite XII a 0.2M concentration in anhydrousacetonitrile was used and the coupling wait time was increased to 300secs (compared to 30 secs for normal nucleotide coupling). Both thesemodifications were necessary to obtain high coupling yields forphosphoramidites V and XII. In each final coupling cycle, the Trityl ONconfiguration was used. After assembly, the oligonucleotides werecleaved from the support using concentrated ammonia at room temperatureusing the manufacturer's end procedure cycle. The ammoniacal solutionwas then heated to 60° C. in a sealed tube for 5 h and evaporated todryness. The residue was dissolved in 0.3 ml acetic acid/water (8:2) andafter 20 minutes at room temperature the mixture was evaporated todryness. To the residue was added water (0.5 ml) and the resultantsuspension filtered. The aqueous solution now contained the deprotectedoligonucleotide ready for h.p.l.c. purification.

EXAMPLE 2 A) Synthesis of Fluorescein PhosphoramiditeFluorescein-5-isothiocyanate-3',6'-dibenzoate

Fluorescein-5'-isothiocyanate (5 g, 12.85 mmole) was dissolved in drypyridine (15 ml). Benzoyl chloride (3 ml, 3.61 g, 25.7 mmole) was addeddropwise over 15 minutes without external cooling and the reactionmixture was stirred in the dark overnight. The reaction was thenpartitioned between ethyl acetate (150 ml) and 5% aqueous sodiumbicarbonate (150 ml). The organic layer was washed twice more withbicarbonate (150 ml each) and with brine (150 ml). TLC over silica(ethyl acetate/pentane 2/1 v/v) showed only one fluorescein containingspot Rf 0.75

Aminopropyl glycerol

3-Aminopropyl solketal (2.43 g 12.8 mmole) was dissolved in THF (30 ml)and aqueous hydrochloric acid (1M, 30 ml) was added. After 1 hour atroom temperature TLC (acetonitrile/methanol/triethlyamine 80/18/2)indicated that all starting material Rf 0.33 had been hydrolyzed to thediol Rf ca.0.0 (detection by ninhydrin spray). THF was evaporated invacuo and the aqueous residue was applied to a Dowex 50 ion exchangecolumn (100 ml, H form). The resin was washed with water to remove allCl ion and the desired amine was eluted with aqueous ammonia. Theammonia solution was evaporated to remove all volatile material and theaqueous residue used for subsequent reactions without furtherpurification.

Dibenzoyl-fluorescein aminopropyl-glyceryl thiourea

Fluorescein-5-isothiocyanate-3',6'-dibenzoate (0.11 mmole) was dissolvedin ethyl acetate/acetonitrile (4/1 v/v) and stirred as a solution ofaminopropyl-glycerol in water (0.11 mmole, 1 ml) was added. After 1 hourstirring at room temperature, TLC (ethyl acetate/pentane 2/1) showedcomplete conversion of starting material (Rf 0.75) to material Rf ca.0.0TLC in a different system (acetonitrile/ethanol 4/1) showed onefluorescein containing spot Rf 0.76 The reaction mixture was washed with5% sodium bicarbonate (2×20 ml) and brine (2×20 ml), dried overanhydrous sodium sulphate and evaporated to dryness to yield a yellowoil.

Dimethoxytrityl-dibenzoyl-fluorescein aminopropyl-glyceryl thiourea

Dibenzoyl-fluorescein aminopropyl-glyceryl thiourea (82 mg, 0.11 mmole)was azeotroped with pyridine (2×20 ml) and dissolved in pyridine.Dimethoxytrityl chloride (60 mg, 0.16 mmole) dissolved in pyridine (10ml) was slowly added to the stirred solution over 40 minutes at roomtemperature and the reaction stirred for a further 20 minutes. Thereaction mixture was concentrated under vacuum and partitioned betweenethyl acetate (50 ml) and 5% aqueous sodium bicarbonate (2×50 ml).TLC(ethyl acetate/pentane 2/1 v/v) showed conversion of all polarmaterial to a spot Rf 0.60. The organic extract was dried over anhydroussodium sulphate, filtered and evaporated. Residual pyridine was removedby azeotrope with toluene (2×10 ml) and the material applied to a silicagel column which was eluted with a gradient of ethyl acetate in pentane(20% to 60%). Fractions containing pure material were combined andevaporated to dryness to yield the product as a pale yellow foam (28mg). Reverse phase hplc (C18 column, 15 cm) showed one single peakretention 8.58 minutes (detector 254 nm). Buffer A=0.1M triethylammoniumacetate 1 Buffer B=acetonitrile. Solvent program 80% B to 95% B over 10minutes, flow 1.0 ml/min, then isocratic for 5 minutes.

Dimethoxytrityl-dibenzoyl-fluorescein aminopropyl-glyceryl thioureadiisopropylamino cyanoethyl phosphoramidite

The dimethoxytrityl compound (1.93 g, 1.85 mmole) was azeotroped withacetonitrile (3×50 ml) and dissolved in dry dichloromethane (50 ml).Cyanoethyl-tetraisopropyl-phosphorodiamidite (0.613 g, 2.03 mmole) wasadded followed by diisopropylammonium tetrazole (0.158 g, 0.925 mmole).The mixture was left to react 1 hour at room temperature and was thenquenched by addition of 50 ml 5% aqueous sodium bicarbonate. The organiclayer was dried by addition of anhydrous sodium sulphate, filtered andevaporated. The resulting yellow oil was dissolved in drydichloromethane (3 ml) and the product precipitated by addition ofpentane (25 ml). The supernatant was decanted and the residual oil driedunder high vacuum to give an off-white foam (1.1 g). Hplc analysisreveals the product as a pair of diastereomers retention times 3.99,4.44 minutes (C18 column, 15 cm, 95% acetonitrile, 5% 1Mtriethylammonium acetate, isocratic, flow 1 ml/minute).

B) Use of a Fluorescein Phosphoramidite to Prepare Oligonucleotides foruse as Hybridization Probes Materials and Methods

Oligonucleotides were assembled using an Applied Biosystems 394-08 4column DNA synthesizer following manufacturers recommendations with thecyanoethyl phosporamidite procedure. The 0.2 umole scale was usedthroughout. For couplings using the fluorescein phosphoramidite a 0.2Mconcentration in anhydrous acetonitrile was used and the coupling waitextended to 300 seconds. Three parallel syntheses were performed of theM13 17-mer forward sequencing primer d(GTAAAACGACGGCCAGT) bearing 1,7and 8 fluorescein labels at the 5' end. In each final coupling thetrityl-on configuration was used.

After synthesis, detritylation was performed as in example 1

Purification of the oligonucleotides was by reverse-phase HPLC on aUltrasphere-ODS column (5 um, 4.6 mm×15 cm) (Beckman Instruments) usinggradients of buffer A (0.1M ammonium acetate) and buffer B (20% bufferA/80% acetonitrile) at flow rates of 1 ml/minute.

M13 mp8 single stranded DNA was spotted (1 ul) onto Hybond N⁺ nylonmembrane (Amersham code 2020B) in dilutions from 20-0.0125 ng/ul in H₂O. A negative control of 50 ng/ul of denatured herring sperm DNA wasalso spotted out. The filters were then baked for 2 hours at 80° C.

Prehybridization of the filters was performed in 0.5% block reagent(ECL-Oligonucleotide labelling system, Amersham, RPN 2111), 0.1%N-lauroylsarcosine (sodium salt), 0.02% SDS, 5×SSC for 30 minutes at 42°C. Hybridizations using the probes labelled with 1 and 7 fluoresceinmolecules at 20 ng/ml were then carried out for 2 hours at 42° C. in thesame buffer. Filters were then washed for 2×15 minutes in 1×SSC, 0.1%SDS at 42° C., followed by a 5 minute wash in 2×SSC at room temperature.

Detection of the fluorescein labelled probes involved blocking of thefilters in 1% block reagent (ECL-Oligonucleotide labelling system,Amersham, RPN 2111). 100 mM Tris-HCL, 150 mM NaCl, pH 7.5 for 60 minutesat 42° C. The filters were then incubated for 30 minutes at roomtemperature in sheep anti-fluorescein antibody conjugated to horseradishperoxidase (ECL 3'-tailing system, Amersham, RPN 2130) diluted 1 in 1000in block buffer. After 4×5 minute washes in 100 mM Tris-HCl. 400 mMNaCl, pH 7.5 at room temperature, detection was carried out using theenhanced chemiluminescent (ECL) detection reagents (Amersham, RPN 2105)followed by exposure to Hyperfilm ECL autoradiography film (Amersham,RPN 2103) for 1 hour.

Results

Efficiency of addition of the fluorescein phosphoramidite averaged 92%as judged by the release of the dimethoxytrityl cation before subsequentcoupling steps.

Purification of the fluorescein labelled oligonucleotide by reversephase HPLC revealed that the fluorescein caused a retardation inmobility compared to unlabelled oligonucleotide. Retention times for the1 and 7 labelled oligonucleotides were 17 and 29 minutes respectively,compared to 16 minutes for the unlabelled oligonucleotide. Theoligonucleotide bearing 8 fluoresceins gave the same retention time asfor the 7 fluorescein probe.

In the detection of single stranded M13 DNA, greater sensitivity wasobserved for the probe bearing 7 fluoresceins than for the probe bearinga single fluorescein. Dection limits after a 1 hour exposure to filmwere 12.5 pg and 100 pg for the 7 and 1 fluorescein probes respectively.

EXAMPLE 3 Materials and Methods Radiolabelling of the BiotinylatedOligonucleotides

The biotinylated oligonucleotides (17-mers) were synthesised asdescribed in example 1. The oligonucleotides corresponded to thesequence of the universal M13 sequencing primer (d(GTAAAACGACGGCCAGT)).Batches of this oligonucleotide were labelled at the 5'-end with 1, 2 or8 biotins using the biotinyl phosphoramidite reagent. After completedeprotection, the three 17-mers had been purified using reverse phasechromatography. A 17-mer, with no biotin label, was obtained from an M13sequencing system (Amersham code N 4502). The four 17-mers were adjustedto 10 pmoles/5 μl and were boiled for 5 min then rapidly chilled on ice.They were then labelled at the 3' end using ³² P-dCTP (Amersham Code PB10205) and a 3'-end Labelling Kit (Amersham Code N 4020). Theradiolabelled 17-mers were then purified from unincorporated dNTPs bycentrifugation down a Sephadex-G25 spin-column.

Capture Assay for the Radiolabelled 17-mers

The assays were performed in white, microtiter plates (DynaTech) withremovable wells. The wells were coated with aliquots (200 μl of asolution of 20 μg ml⁻¹) of either streptavidin (Amersham Code RPN 1041)in TBS (per liter: Tris base, 2.42 g; NaCl, 8 g; 1M HCl, 3.8 ml; pH 7.6)or a mouse monoclonal antibody against biotin in 0.1Mcarbonate/bicarbonate buffer (pH 9.5) and incubated at 4° C. overnight.The wells were then washed three times in TBS with 0.1% (v/v) Tween-20(TBST). Aliquots (200 μl) of blocking solution (TBS with 0.1% (w/v)bovine serum albumin) were then added and the plate incubated for 1 h at37° C. After washing three times with TBST solution, aliquots (200 μl)of oligonucleotide solution were added to each appropriate well and theplate re-incubated for 1 h at 37° C. Following incubation, the wellswere again washed three times in TBST and the final wash solutionremoved. Each well was then placed in separate scintillation vials andassayed by Cerenkov counting. % Capture was determined using thefollowing equation: ##EQU1##

RESULTS

The objective of the experiment was to monitor capture of anoligonucleotide labelled with biotinyl phosphoramidite residues usingeither streptavidin or an anti-biotin antibody to capture thebiotin-oligonucleotide onto the solid phase of a microtiter well. By3'-radiolabelling the oligonucleotides the efficiency of capture couldbe determined using scintillation counting of the wells.

Experiment 1

In this experiment approximately 2×10¹³ radiolabelled oligonucleotidemolecules were added per well. The results suggested that capture wasoccurring and that with the anti-biotin antibody there was a correlationbetween increasing biotin tail length and its efficiency of capture(FIG. 8). Although there also appeared to be a similar correlation withstreptavidin as the capturing agent, the increase in capture efficiencywith increased biotin tail length was less than that with antibodycapture.

Experiment 2

In this experiment approximately 2.4×10¹² oligonucleotide molecules wereadded per well. The results from experiment 1 were verified and thebiotin-labelled oligonucleotides were captured at levels significantlyabove background (oligonucleotide with no biotin label) suggesting thatthe biotin label was being captured (FIG. 9).

EXAMPLE 4 Solid Phase sequencing of DNA generated by the PolymeraseChain Reaction (PCR)

The protocol is based on the method of Hultmann T., et al (1989) NucleicAcids Research 17, pp.4937-4946. Specific target DNA is amplified by PCRusing one biotinylated primer and one non-biotinylated primer. Theamplified DNA is captured via the biotin by streptavidin linked to asolid phase (in this example, a magnetic bead). The non-biotinylatedstrand is then removed by alkali. Either the bound strand or thenon-bound strand can then be sequenced using standard protocols.

Materials and Methods Amplification by the Polymerase Chain Reaction

Biotinylated primer oligonucleotides were synthesised as described inExample 1. The template DNA (typically 1-2 pmols of target sequence) wasamplified in 50 μl containing 10 mM Tris-HCl, pH9.5, 50 mM NaCl, 3 mMMgCl2, 0.01% NP-40, 0.05% gelatin, 250 μM each of dATP, dCTP, dGTP anddTTP, 5 pmoles of biotinylated primer 1, 5 pmoles of non-biotinylatedprimer 2 and 2 u of Taq polymerase (Amersham code T0303Y). The reactionswere cycled for 30 cycles of 94° C. for 45 seconds, 45° C. for 45seconds and 72° C. for 2 minutes.

Preparation of Single Stranded Template

Immediately prior to use, the streptavidin coated beads (Dynal, M-280streptavidin) were washed for 2×5 minutes in 0.1M NaCl. The beads wereresuspended after washing at a concentration of 10 mg/ml in 0.1M NaCl.

50 μl of washed beads were added to a fresh tube and the beadsseparated. The completed PCR mix was used to resuspend the beads and thetube was incubated for 30-60 minutes at room temperature with mixing.The beads were then separated and washed with 200 μl of water.

Single stranded template was prepared by incubating the beads coatedwith PCR DNA in 20 μl of 0.15M NaOH for 5 minutes at room temperature.The beads were then separated and washed once with 200 μl of 0.15M NaOHand then twice with 200 μl of water. The beads were finally resuspendedin 30 μl of water.

Sequencing of Solid Phase DNA

The solid phase bound template was sequenced exactly as single strandedtemplate using the T7 polymerase Multiwell microtiter plate sequencingsystem (Amersham, code RPN1590).

The sequencing reactions were denatured prior to loading on a standard6% sequencing gel by heating at 95° C. for 5 minutes. At this point, thebeads can be separated and the supernatant loaded on the gel.

Electrophoresis and subsequent processing of the sequencing gel wereexactly as standard protocols.

EXAMPLE 5 Use of Primers Labelled with Biotinyl or PhosphotyrosinylPhosphoramidite in Sequencing Reactions Materials and Methods

Primer oligonucleotides were labelled with biotin or phosphotyrosine asin Example 1. The primers were used at a concentration of 0.12 OD/ml(-0.8 μM) in row 3 of a T7 Multiwell plate. All other procedures were asstandard for the T7 Multiwell System (Amersham, code RPN1590).

EXAMPLE 6 Direct Enhanced Chemiluminescence (ECL) Detection of BlottedSequencing Ladders Using Labelled Primers Materials and Methods

Sequencing Reactions

The reactions were performed as in example 5. Single stranded M13mp8(Amersham, code N4526) was used as template at 3 μg per sequencingreaction. [³⁵ S]dATPαS was included in the sequencing reaction to assessthe quality of the sequencing ladder before and after transfer.

Blotting of Sequencing Gel

The preparation, pre-running and running of the sequencing gel wasexactly as standard protocols.

After electrophoresis, the sequencing ladder was blotted as follows. Theglass plates were separated and a sheet of filter paper was placed onthe gel surface such that no air bubbles were trapped between gel andpaper. The gel was then lifted from the glass plate and placed paperside down on a clean, flat surface.

A piece of nitrocellulose membrane (Hybond C-extra, Amersham, codeRPN303E) was prewet in 50 mM ammonium acetate (AmAc) and was thencarefully laid onto the gel, again taking care that no air bubbles weretrapped between the gel and membrane. A sheet of filter paper was thenlaid on top of the membrane, again ensuring that all air bubbles wereremoved. Excess membrane and filter paper were then trimmed from theedges of the gel.

The gel sandwich was then inverted and placed on a stack of paper towelsthat had previously been soaked in 500 mM AmAc and dried (in an oven at50° C.). On top of the gel, towels soaked in 50 mM AmAc were layered. Aflat perspex sheet and weights of about 1 kg were then placed on top ofthe wet towels. The transfer was allowed to proceed overnight.

After blotting, the membrane and gel were seperated and the DNA wasfixed to the membrane by placing the blot on a vacuum gel drier for 2hours at 80° C. The blot was then autoradiographed to assess theefficiency of transfer of the sequencing ladder.

Detection of the Sequencing Ladder using Streptavidin-HRP and ECL

The membrane with the transferred sequencing ladder was treated asfollows.

The membrane was blocked by incubation for 1 hour in PBS-Tween (0.05%)containing 5% non-fat milk. After washing for 6×5 minutes in PBS-Tween(0.05%), the membrane was incubated for 60-90 minutes withStreptavidin-biotinylated HRP complex (RPN1051) diluted 1:1000 inPBS-Tween (0.05%).

After washing for 6×5 minutes in PBS-Tween (0.05%), the sequencingladder was detected using=ECL as described in the ECL Gene DetectionSystem (Amersham, code RPN2101).

EXAMPLE 7 Use of Biotinyl and Phosphotyrosinyl Phosphoramidites forpreparing Oligonucleotides for use as Hybridisation Probes (extractedfrom Misiura, K. et al (1990) Nucleic Acids Research, 18: pp.4345-54)Materials and Methods

M13 sequencing primers labelled with biotin or phosphotyrosine wereprepared as in Example 1.

M13mp19 single-stranded DNA was spotted on pre-wet (water, then 1Mammonium acetate solution) nitrocellulose filters (Schleicher andSchuell) in serial dilutions in 10 mM Tris HCl (pH 7.4), 5 mM NaCl, 0.1mM EDTA (amounts 0.05-50 ng). The filters were baked at 80° C. for 1hour and washed in 6XSSC, 0.2% BSA, 0.2% PVP 40, 0.2% Ficoll 400, 0.2%SDS at 60° C. for 10 mins. After brief rinsing in 6XSSC, hybridisationwas carried out in solutions of biotinylated or phosphotyrosinylatedoligomers (10 nM) at 37° C. for 2 hours. Filters were washed in 2XSSC,0.1% SDS twice for 1 minute and then for 1 minute in 2XSSC.

Quantitative detection of biotinylated probes involved blocking of thefilter with 5% w/v reconstituted milk powder in TBST (Tris bufferedsaline plus 0.05% Tween 20) for 1 hour, incubation with a mousemonoclonal antibody against biotin (0.1 μg/ml in TBST), washing withTBST (6×5 mins) and then incubation with sheep anti-mouseIgG-horseradish peroxidase conjugate (Amersham, code NA 931) at a 1/1000dilution in TBST. After washes with TBST (6×5 mins) and TBS (1×5 min),detection was carried out using the enhanced chemiluminescent (ECL)detection reagents (Amersham, code RPN 2105). The still moist filterswere photographed and quantitated using a CCD camera (600 secondexposures). Control 17-mer oligonucleotide directly linked tohorseradish peroxidase was prepared using the ECL oligonucleotidelabelling and detection system (Amersham code, RPN 2111/2113).

Phosphotyrosine-labelled probes were detected quantitatively using theECL method. Primary detection was by a mouse monoclonal antibody againstphosphotyrosine (0.5 μg/ml) and the secondary antibody was sheepanti-mouse IgG conjugated to horseradish peroxidase (Amersham, CodeNA931) used at 1/1000 dilution.

Results

As the number of biotin residues in the probe was increased, there was asubstantial increase in signal strength in detection of M13 DNA (FIG.14). Spacing of biotin with thymidinyl residues resulted in a 50%increase in signal strength compared to the unspaced probe at this M13DNA concentration. In addition, the sensitivity of detection usingeither the (bio)₈ -17 probe or the spaced (bio-dT)₃ -bio-17 probe wasvery similar to that obtained with the same 17-mer directly conjugatedto horseradish peroxidase.

There was also a significant increase in signal strength obtained as thenumber of phosphotyrosinyl residues was increased (FIG. 11), althoughthe effect was less pronounced than in the case of biotinylatedoligonucleotides. Spacing of phosphotyrosine with thymidinyl residuesresulted in a slight decrease in signal strength compared to theunspaced probe.

Using the ECL system and biotinylated or phosphotyrosinylated probes, alinear logarithmic response was observed between the amount of lightproduced and the amount of M13 DNA spotted on the filter. (Misiura, K.et al, (1990) Nucleic Acid Research, 18, pp.4345-54).

References

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We claim:
 1. A phosphoramidite derivative of the following formula:##STR15## wherein X=biotin, andY=a protecting group.
 2. Aphosphoramidite derivative as claimed in claim 1, wherein there is alinker arm of variable length between biotin and the rest of themolecule.
 3. A phosphoramidite derivative as claimed in claim 1, whereinY is 4,4'-dimethoxytrityl.
 4. A method for the production of aphosphoramidite derivative of the following formula: ##STR16## and whichcomprises: i) Reaction of solketal with acrylonitrile to form theaddition product, 2-cyanoethyl solketal (I): ##STR17## ii) Reduction ofthe resultant compound (I) to form 3-aminopropyl solketal (II):##STR18## iii) Reaction of the resultant compound (II) with biotinN-hydroxysuccinimide to form N-biotinyl-3-aminopropyl solketal (III):##STR19## iv) Reaction of the resultant compound (III) with4,4'-dimethoxytrityl chloride to form 1-0-(4,4'-dimethoxytrityl)-3-0-(N-biotinyl-3-aminopropyl) glycerol (IV):##STR20## v) Phosphitylation of the resultant compound (IV) to producethe desired biotinyl phosphoramidite derivative (V): ##STR21## whereinDMTr=4,4'-dimethoxytrityl.
 5. A method for the single or multiplelabelling of synthetic oligonucleotides and which comprises the use of aphosphoramidite ligand as claimed in claim
 1. 6. A method for the singleor multiple labeling of synthetic oligonucleotides and which comprisesthe use of a phosphoramidite ligand as claimed in claim 1, wherein thelabeling with said phosphoramidite ligand occurs at the 5' end or the 3'end of the oligonucleotide or at any internal position along the chain.